List of works by Buyong Ma

"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains

scientific article published on December 2006

A Molecular Mechanics Study of the Cholesteryl Acetate Crystal: Evaluation of Interconversion amongrg,rz, andrαBond Lengths

scientific article published in 1997

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery

scientific article published on 03 January 2013

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core

scientific article

Allosteric conformational barcodes direct signaling in the cell

scientific article published on September 2013

Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains

scientific article published on 29 November 2016

Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD

scientific article

Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal

scientific article

Amplification of signaling via cellular allosteric relay and protein disorder

scholarly article

Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease

scientific article

Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42

scientific article published on 06 May 2008

Antigen binding allosterically promotes Fc receptor recognition

scientific article published on 05 October 2018

Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition.

scientific article published on 8 February 2018

Aβ(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease

scientific article published on 4 May 2015

Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations

scientific article

Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning

scientific article published on 5 October 2017

Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs

scientific article

CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible

scientific article

Calculation of rz structures from rs structures

Carbon monoxide in controlling the surface formation of Group VIII metal nanoparticles.

scientific article published in November 2014

Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain

scientific article

Comparison of the human and worm p53 structures suggests a way for enhancing stability

scientific article

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface

scientific article

Computational Investigation of Gantenerumab and Crenezumab's Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue

scientific article published on 29 September 2020

Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau.

scientific article

Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer

scientific article published on 16 December 2013

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization

scientific article published on 8 August 2016

Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes

scientific article published on 3 June 2016

Conformational stability and dynamics of the cancer-associated isoform Δ133p53β are modulated by p53 peptides and p53-specific DNA

scientific article published on 12 December 2018

Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect

scientific article

Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure

scientific article

Conservation of polar residues as hot spots at protein interfaces

scientific article

Conservation of polar residues as hot spots at protein interfaces

scholarly article by Zengjian Hu published in June 2000

Contribution of salt bridges toward protein thermostability

scientific article

Cooperativity among short amyloid stretches in long amyloidogenic sequences

scientific article

Correction to Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils

scientific article published on 01 June 2018

Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization.

scientific article

Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the α-synuclein fibrils

scientific article

Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein

scientific article

Cross-seeding and conformational selection between three- and four-repeat human Tau proteins

scientific article published on 5 March 2012

Crystal structure of a plectonemic RNA supercoil

scientific article

Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein

scientific article

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly

scientific article published on 4 December 2015

Dipeptide analysis of p53 mutations and evolution of p53 family proteins.

scientific article published on 10 April 2013

Disruption of the Rbm38-eIF4E Complex with a Synthetic Peptide Pep8 Increases p53 Expression

scientific article published on 27 December 2018

Druggable orthosteric and allosteric hot spots to target protein-protein interactions.

scientific article published on January 2014

Dynamic allostery: linkers are not merely flexible

scientific article published on July 2011

Dynamics differentiate between active and inactive inteins

scientific article

Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein.

scientific article published on 8 October 2015

Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences

scientific article published on September 2003

Enzyme dynamics point to stepwise conformational selection in catalysis ⬇️

scientific article published on September 6, 2010

Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies.

scientific article published in January 2018

Explicit and implicit water simulations of a ?-hairpin peptide

scholarly article by Buyong Ma published in October 1999

Explicit and implicit water simulations of a beta-hairpin peptide

scientific article

Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils

scientific article published on 11 January 2017

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

scientific article published in 2022

Folding and binding cascades: shifts in energy landscapes

scientific article

Fragmentation surface of triplet ketene

article published in 1998

From computational quantum chemistry to computational biology: experiments and computations are (full) partners

scientific article

From structure to function: methods and applications

scientific article

Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH.

scientific article

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues

scientific article

How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability?

scientific article published on 8 February 2016

How do transcription factors select specific binding sites in the genome?

scientific article published in November 2009

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues

scientific article

Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity

scientific article published on 28 December 2016

IKKα inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways

scientific article published on 8 January 2018

In Silico Methods in Antibody Design

scientific article published on 29 June 2018

In silico protein design by combinatorial assembly of protein building blocks

scientific article published on October 2004

In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1.

scientific article

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.

scientific article published on April 2016

Insights into amyloid structural formation and assembly through computational approaches

scientific article

Interaction of protegrin-1 with lipid bilayers: membrane thinning effect

scientific article

Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I.

scientific article

Interface-Based Structural Prediction of Novel Host-Pathogen Interactions

scientific article published on 01 January 2019

Intermolecular disulfide bonds between unpaired cysteines retard the C-terminal trans-cleavage of Npu DnaE

scientific article published on 03 July 2018

Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control

scientific article published on 4 February 2009

Investigation of the interactions between the EphB2 receptor and SNEW peptide variants

scientific article

Is allostery an intrinsic property of all dynamic proteins?

scientific article published in November 2004

Ligand binding and circular permutation modify residue interaction network in DHFR.

scientific article

Local and global anatomy of antibody-protein antigen recognition

scientific article published on 8 December 2017

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

scientific article published on September 2015

Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies

scientific article published on 18 September 2017

Mechanisms of transcription factor selectivity

scientific article published on 13 January 2010

Metal binding sites in amyloid oligomers: Complexes and mechanisms

Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities

scientific article

Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels

scientific article published on 15 August 2008

Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates

scientific article published on 13 July 2018

Molecular dynamics based improvement of the solubilizing self-cleavable tag Zbasic-ΔI-CM application in the preparation of recombinant proteins in Escherichia coli.

scientific article published on 6 April 2019

Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations

scientific article

Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association.

scientific article

Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces

scientific article

Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation

scientific article published on October 2002

Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants

scientific article published in August 2003

Molecular insights into the reversible formation of tau protein fibrils

scientific article published on May 2013

Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy

scientific article

Multiple conformational selection and induced fit events take place in allosteric propagation.

scientific article published on 31 October 2013

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

scientific article

Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment

scientific article

Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain

scientific article published on February 2009

Network effect of Wt-mutant p53 interactions and implications on p53 gene therapy

scientific article published on January 2014

Nuclease activity gives an edge to host-defense peptide piscidin 3 over piscidin 1, rendering it more effective against persisters and biofilms.

scientific article published on 30 September 2017

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

scientific article published on 15 September 2016

Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites

scientific article published in Journal of Biological Chemistry

Peptide-MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs)

scientific article published on 03 November 2020

Periodic Trends for Transition Metal Dihydrides MH2, Dihydride Dihydrogen Complexes MH2·H2, and Tetrahydrides MH4(M = Ti, V, and Cr)

scientific article published in 1996

Polymophism of A-Beta1-42 Peptide Oligomer - Membrane Interactions

Polymorphic C-terminal β-Sheet Interactions Determine the Formation of Fibril or Amyloid β-derived Diffusible Ligand-like Globulomer for the Alzheimer Aβ42 Dodecamer ⬇️

scientific article published on September 16, 2010

Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide

scientific article

Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape

scientific article

Polymorphism in self-assembly of peptide-based β-hairpin contributes to network morphology and hydrogel mechanical rigidity

scientific article

Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation

scientific article published on August 2009

Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer

scientific article

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

scientific article

Principles of docking: An overview of search algorithms and a guide to scoring functions

scientific article (publication date: June 2002)

Principles of docking: An overview of search algorithms and a guide to scoring functions

scholarly article by Inbal Halperin published in May 2002

Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

scientific article published on 21 March 2008

Probing Oligomerized Conformations of Defensin in the Membrane.

scientific article published in January 2017

Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements

scientific article

Promiscuous and specific recognition among ephrins and Eph receptors

scientific article

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

scientific article published on 25 January 2016

Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome

scientific article published on 18 March 2013

Protein dynamics and conformational selection in bidirectional signal transduction

scientific article

Protein dynamics: Conformational footprints.

scientific article published in October 2016

Protein functional epitopes: hot spots, dynamics and combinatorial libraries

scientific article

Protein-protein interaction networks: how can a hub protein bind so many different partners?

scientific article published on December 2009

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking

scientific article

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

scientific article

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces

scientific article

R102Q mutation shifts the salt-bridge network and reduces the structural flexibility of human neuronal calcium sensor-1 protein

scientific article published on 7 November 2014

Recent Progress in Antibody Epitope Prediction

scientific article published in 2023

Regulating highly dynamic unstructured proteins and their coding mRNAs

scientific article (publication date: 2009)

Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes

scientific article published on 8 October 2004

Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane

scientific article

Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example

scientific article published on 01 January 2018

Selective molecular recognition in amyloid growth and transmission and cross-species barriers

scientific article published on 19 November 2011

Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.

scientific article published on 29 February 2016

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets

scientific article published on 16 April 2007

Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL

scientific article

Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19.

scientific article

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation

scientific article published on 28 August 2006

Single mutations in tau modulate the populations of fibril conformers through seed selection

scientific article

Singlet-triplet energy separation and barrier for ring closure for trimethylenemethane and its complexes

Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects

scientific article

Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation

scientific article

Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.

scientific article published on 17 April 2012

Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms

scientific article published in Journal of Biological Chemistry

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.

scientific article

Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients

scientific article

Structured crowding and its effects on enzyme catalysis.

scientific article published on January 2013

Structured disorder and conformational selection

scientific article

Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states

scientific article

Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

scientific article

The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins

scientific article

The distinct structural preferences of tau protein repeat domains

The origin of allosteric functional modulation: multiple pre-existing pathways

scientific article published on August 2009

The stability and dynamics of the human calcitonin amyloid peptide DFNKF

scientific article

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant

scientific article

The underappreciated role of allostery in the cellular network.

scientific article

The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions

scientific article

Theoretical Studies of the Potential Energy Surfaces and Compositions of thed-Aldo- andd-Ketohexoses

scientific article (publication date: April 1998)

Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway

scientific article published on February 2002

Toward the observation of silanone (H2SiO) and hydroxysilylene (HSiOH) via microwave spectroscopy

Towards drugs targeting multiple proteins in a systems biology approach

scientific article

Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?

scientific article

Triggering loops and enzyme function: identification of loops that trigger and modulate movements

scientific article published in September 2003

Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design

scientific article published on January 2007

Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?

scientific article

Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states

scientific article

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